The £100,000 of unpaid bills found by investigators on a desk in a Norfolk comprehensive earlier this year should ring alarm bells in Westminster. The headteacher had appeared an ideal leader, ambitious for her pupils, keen to help the school raise its game and to do so without the help of her local authority. But, last year, she was suspended and this summer, resigned, leaving behind nearly £1m of debt. What went wrong?

The school's plight is, arguably at least, the result of the drip-drip message that the most successful heads are those who relish going it alone. For Michael Gove, the education secretary, it is axiomatic that autonomy drives up performance. Many agree with him. Tony Blair, who set up the original academies in 2000, wrote this year of schools gaining "pride and purpose" from being in charge of their own destiny, free from "the extraordinarily debilitating and often, in the worst sense, politically correct interference from state or municipality".

Yet autonomy brings risks. According to Malcolm Trobe, of the Association of School and College Leaders (ASCL): "The movement towards academies leaves heads significantly more vulnerable than they used to be. If something goes wrong, it is going to come back on the leadership team and on the head. They are isolated, they have cut off any support mechanisms they might have had from the local authority."

Encouraging heads to fly solo runs counter to recent moves away from the model of "the heroic leader riding in to save a school on his or her white charger", according to Peter Earley, professor of educational leadership and management at London's Institute of Education. "We were hearing more about distributed or shared leadership, but now it seems it is only to be shared within the school and not with the local authority, the governors, or fellow heads. It is a competitive rather than collaborative model."

Heads have long been under pressure to raise standards. These days the expectation is that they will do it quickly – and cheaply. It is perhaps no coincidence that the ASCL talks of a five-fold increase in the number of heads leaving their jobs prematurely. Trobe says the number of suspensions is also rising, from about 50 secondary heads in 2008 to 70 last year.

One of those suspended heads was Yve Srodzinski. She took over Hamond's high school in Swaffham, Norfolk, in 2002. It was her first headship. An ambitious £13m refurbishment of the comprehensive was soon under way. A new-style school business manager was employed. He was not an accountant, but a former soldier who had served as head of administration for the British Embassy in Washington as well as for an SAS unit.

Before long the school was out on a limb. According to a former employee, "She [Srodzinski] deliberately distanced herself from the county council. She took payroll management away from it, which she was entitled to do, but it meant the county had no idea who was employed or on what grade. She used a Serco computer system when most of Norfolk was on Phoenix. She employed expensive consultants. One firm was to help with lesson plans, but teachers refused to use it when they realised their material would become its property. It cost thousands to get out of the contract."

The school no longer employed "the respected and cheap" local authority advisory service, says the ex-employee. Instead, it signed a three-year contract with a private company to improve exam results. "We had lots of former teachers, inspectors and advisers wandering around, all in very smart suits." But the grades did not improve – bumping along at 38% five A*-C grade GCSEs for three years in a row. In 2006, and again in 2009, Ofsted deemed Hamond's merely satisfactory.

"The atmosphere was awful," says the former employee. "The school's sense of community had been destroyed. Everything was blamed on the teachers. Staff turnover was high." Then, in April 2009, Srodzinski was suspended pending an investigation into management issues.

Hamond's, nearly £1m in the red, was deprived of the right to manage its own accounts. The county took back control, alarmed at discoveries such as the £100,000 of unpaid bills sitting waiting for the start of the new financial year – a "totally unacceptable practice", says Paul Fisher, assistant director of Norfolk's children's services. Finally, this summer, a bleak three-sentence letter on the school website announced the head's decision to "step aside". Attempts by Education Guardian to contact Srodzinski were not successful.

The burden of the debt – and that of another Norfolk school that went £730,000 into the red – has had to be borne by the rest of the county's schools. The county council now runs a termly check on schools' budgets. In doing so, says Fisher, it discovered a deterioration in financial management, so a policy of "supportive interference" has been agreed with heads: "It's a case of get in there before it goes bad." The consequences of a head who "wished to be totally independent of its help" have been painfully illuminating.

Too many heads are not good at strategic financial management, says Trobe, adding that it is a weakness the National Professional Qualification for Headship is failing to tackle. With more schools running deficit budgets, he foresees this becoming an increasing problem, though not one that should surprise anyone. The National College for Leadership noted in 2008 that would-be heads felt "least confident in securing budget and financial accountabilities". Earlier this year, the Audit Commission urged MPs to tighten up the scrutiny of financial management in schools, a call echoed recently by the National Audit Office, which reported that a quarter of academies had needed bail-outs to balance their books.

Nevertheless, this summer Michael Gove relaxed the requirement that the finance directors of academies must be accountants. This worries David Waller, who runs School Accounting and Finance Services, a private company. "Heads are not adequately trained in either the theory or practice of running school budgets; they tend to have to learn on the job." He bemoans the dearth of audits. "Schools should be audited regularly, not because they are likely to defraud the public exchequer, but because it reassures them that they are doing things properly."

The detail s of what was not done properly at Hamond's are secret, locked up behind the now routine gagging clauses written into deals between outgoing heads and local authorities – a "very murky area", according to Earley. Usually the news of a suspended head merits only a brief mention in the local paper, the story drying up when both sides clam up. Parents and public are often left permanently in the dark as to what went on.

Such secrecy is unhealthy. In 2004, for example, Barrie Cooper, head of Chulmleigh community college in Devon, was suspended for reasons that are still unclear to many parents. He resigned and quickly picked up a new headship in Lichfield. Four years later, he was appointed principal of the £25m West Lakes academy in Cumbria. After less than a year in post, the academy's governors suspended him. An inquiry found evidence of gross misconduct. It was only after that inquiry, which resulted in Cooper getting a £45,000 payoff, that his earlier suspension came to light.

Norfolk admits that staffing costs at Hamond's spiralled out of control. "Heads sometimes forget that they have to tailor their staffing to their resources," says Fisher. Trobe agrees: "It's always staffing costs. ASCL consultants work with quite a few schools in a financial pickle. Some of these are very successful. They use lots of strategies to raise standards and they employ loads of staff – and they can't afford to pay for them."

Taking on a challenging school such as Hamond's is an even riskier business, says Trobe, certainly when you add in the government expectation that improvement should be visible after a year. "You cannot turn a school round quickly. You can have some initial impact, you can do some patches on exam performance, but to make it sustainable takes time. Heads cannot do it on their own, they need a good leadership team and good teachers. People will take on the job if there are big bucks involved and that's fair enough. After all ,they're taking a risk with their career." Not to mention those of their staff and pupils.

Hamond's is currently being led by interim head Stuart Bailey. He says the school is improving steadily, the county council has been enormously supportive and the issue of "flying solo" has no relevance to him.